Dataset Information

IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction.

ABSTRACT: Non-coding RNAs (ncRNAs) play crucial roles in many biological processes, such as post-transcription of gene regulation. ncRNAs mainly function through interaction with RNA binding proteins (RBPs). To understand the function of a ncRNA, a fundamental step is to identify which protein is involved into its interaction. Therefore it is promising to computationally predict RBPs, where the major challenge is that the interaction pattern or motif is difficult to be found.In this study, we propose a computational method IPMiner (Interaction Pattern Miner) to predict ncRNA-protein interactions from sequences, which makes use of deep learning and further improves its performance using stacked ensembling. One of the IPMiner's typical merits is that it is able to mine the hidden sequential interaction patterns from sequence composition features of protein and RNA sequences using stacked autoencoder, and then the learned hidden features are fed into random forest models. Finally, stacked ensembling is used to integrate different predictors to further improve the prediction performance. The experimental results indicate that IPMiner achieves superior performance on the tested lncRNA-protein interaction dataset with an accuracy of 0.891, sensitivity of 0.939, specificity of 0.831, precision of 0.945 and Matthews correlation coefficient of 0.784, respectively. We further comprehensively investigate IPMiner on other RNA-protein interaction datasets, which yields better performance than the state-of-the-art methods, and the performance has an increase of over 20 % on some tested benchmarked datasets. In addition, we further apply IPMiner for large-scale prediction of ncRNA-protein network, that achieves promising prediction performance.By integrating deep neural network and stacked ensembling, from simple sequence composition features, IPMiner can automatically learn high-level abstraction features, which had strong discriminant ability for RNA-protein detection. IPMiner achieved high performance on our constructed lncRNA-protein benchmark dataset and other RNA-protein datasets. IPMiner tool is available at http://www.csbio.sjtu.edu.cn/bioinf/IPMiner .

SUBMITTER: Pan X

PROVIDER: S-EPMC4979166 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction.

Pan Xiaoyong X Fan Yong-Xian YX Yan Junchi J Shen Hong-Bin HB

BMC genomics 20160809

<h4>Background</h4>Non-coding RNAs (ncRNAs) play crucial roles in many biological processes, such as post-transcription of gene regulation. ncRNAs mainly function through interaction with RNA binding proteins (RBPs). To understand the function of a ncRNA, a fundamental step is to identify which protein is involved into its interaction. Therefore it is promising to computationally predict RBPs, where the major challenge is that the interaction pattern or motif is difficult to be found.<h4>Results ...[more]

PMID: 27506469

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Project description:BackgroundIdentification of protein interacting sites is an important task in computational molecular biology. As more and more protein sequences are deposited without available structural information, it is strongly desirable to predict protein binding regions by their sequences alone. This paper presents a pattern mining approach to tackle this problem. It is observed that a functional region of protein structures usually consists of several peptide segments linked with large wildcard regions. Thus, the proposed mining technology considers large irregular gaps when growing patterns, in order to find the residues that are simultaneously conserved but largely separated on the sequences. A derived pattern is called a cluster-like pattern since the discovered conserved residues are always grouped into several blocks, which each corresponds to a local conserved region on the protein sequence.ResultsThe experiments conducted in this work demonstrate that the derived long patterns automatically discover the important residues that form one or several hot regions of protein-protein interactions. The methodology is evaluated by conducting experiments on the web server MAGIIC-PRO based on a well known benchmark containing 220 protein chains from 72 distinct complexes. Among the tested 218 proteins, there are 900 sequential blocks discovered, 4.25 blocks per protein chain on average. About 92% of the derived blocks are observed to be clustered in space with at least one of the other blocks, and about 66% of the blocks are found to be near the interface of protein-protein interactions. It is summarized that for about 83% of the tested proteins, at least two interacting blocks can be discovered by this approach.ConclusionThis work aims to demonstrate that the important residues associated with the interface of protein-protein interactions may be automatically discovered by sequential pattern mining. The detected regions possess high conservation and thus are considered as the computational hot regions. This information would be useful to characterizing protein sequences, predicting protein function, finding potential partners, and facilitating protein docking for drug discovery.

Project description:Background and objectiveIncreases in outpatients seeking medical check-ups are expanding the number of health examination data records, which can be utilized for medical strategic planning and other purposes. However, because hospital visits by outpatients seeking medical check-ups are unpredictable, those patients often cannot receive optimal service due to limited facilities of hospitals. To resolve this problem, this study attempted to predict re-visit patterns of outpatients.MethodTwo-phase sequential pattern mining (SPM) and an association mining method were chosen to predict patient returns using sequential data. The data were grouped according to the outpatients' personal information and evaluated by a discriminant analysis to check the significance of the grouping. Furthermore, SPM was employed to generate frequency patterns from each group and extract a general association pattern of return.ResultsResults of sequence patterns and association mining in this study provided valuable insights in terms of outpatients' re-visit behaviors for regular medical check-ups. Cosine and Jaccard are two symmetric measures which were used in this study to indicate the degree of association between two variables. For instance, Jaccard values of variable abnormal blood pressure associated with an abnormal body-mass index (BMI) and/or abnormal blood sugar were respectively 47.5% and 100%, for the two-visit and three-visit behavior patterns. These results indicated that the corresponding pair of variables was more reliable when covering the three-visit behavior pattern than the two-visit behavior. Thus, appropriate preventive measures or suggestions for other medical treatments can be prepared for outpatients that have this pattern on their third visit. The higher degree of association implies that the corresponding behavior pattern might influence outpatients' intentions to regularly seek medical check-ups concerning the risk of stroke. Furthermore, a radiology diagnosis (i.e., magnetic resonance imaging or neck vascular ultrasound) plays an important role in the association with a re-visit behavior pattern with respective 50% and 70% Cosine and Jaccard values in general behavior {f11}∧{f01}. These findings can serve as valuable information to increase the quality of medical services and marketing, by suggesting appropriate treatment for the subsequent visit after learning the behavior patterns.ConclusionsThe proposed method can provide valuable information related to outpatients' re-visit behavior patterns based on hidden knowledge generated from sequential patterns and association mining results. For marketing purposes, medical practitioners can take behavior patterns studied in this paper into account to raise patients' awareness of several possible medical conditions that might arise on subsequent visits and encourage them to take preventive measures or suggest other medical treatments.

Project description:BackgroundMany studies report about detection and functional characterization of cis-regulatory motifs in untranslated regions (UTRs) of mRNAs but little is known about the nature and functional role of their distribution. To address this issue we have developed a computational approach based on the use of data mining techniques. The idea is that of mining frequent combinations of translation regulatory motifs, since their significant co-occurrences could reveal functional relationships important for the post-transcriptional control of gene expression. The experimentation has been focused on targeted mitochondrial transcripts to elucidate the role of translational control in mitochondrial biogenesis and function.ResultsThe analysis is based on a two-stepped procedure using a sequential pattern mining algorithm. The first step searches for frequent patterns (FPs) of motifs without taking into account their spatial displacement. In the second step, frequent sequential patterns (FSPs) of spaced motifs are generated by taking into account the conservation of spacers between each ordered pair of co-occurring motifs. The algorithm makes no assumption on the relation among motifs and on the number of motifs involved in a pattern. Different FSPs can be found depending on different combinations of two parameters, i.e. the threshold of the minimum percentage of sequences supporting the pattern, and the granularity of spacer discretization. Results can be retrieved at the UTRminer web site: http://utrminer.ba.itb.cnr.it/. The discovered FPs of motifs amount to 216 in the overall dataset and to 140 in the human subset. For each FP, the system provides information on the discovered FSPs, if any. A variety of search options help users in browsing the web resource. The list of sequence IDs supporting each pattern can be used for the retrieval of information from the UTRminer database.ConclusionComputational prediction of structural properties of regulatory sequences is not trivial. The presented data mining approach is able to overcome some limits observed in other competitive tools. Preliminary results on UTR sequences from nuclear transcripts targeting mitochondria are promising and lead us to be confident on the effectiveness of the approach for future developments.

Dataset Information

IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction.

Publications

IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction.

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